Since I got the iPad, I have been reading more PDF-type stuff. I was keeping it separate in its own little PDF folder because I was worried large files would gum up Calibre, which has never been very speedy on my machine and is already pushing 900 entries just of novels and proper books. But it is getting out of hand, I am finding it hard to locate things swiftly and identify what is on the iPad and what is not. I have too many sub-folders. It is getting unwieldy.

I don't want to convert these files or use Calibre features like that. I just want to have them all in one central place where I can search, sort and load onto iBooks. Most of them are magazine scans, and a few textbook-type stuff. Some of them are short (specific magazine articles I have scanned) and some are full-length books.

If Calibre is not the solution, is there something else? Or should I just put them into Calibre with the rest of my ebook stuff?

Calibre, if allowed to do its own thing, doesn't organize files, folders, etc. It organizes books. It doesn't care about file or filename size. As long as your OS can handle the filename, so can calibre.

The thing that people have the hardest time understanding about calibre is calibre uses tags to keep track of books and organnizes them within the program instead of in an OS' folder and file hiearchy, which is one reason why calibre copies books from the user's location to its own folder with a simplified file and folder structure.

I feel (and apparently do you) that you are unnecessarily complicating your use of calibre. Unless your PDFs are something radically different from your e-books, such as technical or legal documents, just put them all together into calibre and let calibre do the sorting. If you want to be able to easily see what format each e-book is in (such as epub or PDF), you can create a custom column in Preferences to show that. Then, if you want a listing of only your PDFs, just do a search.

The hardest part people have with letting calibre doing all the sorting, etc., is that calibre uses a simplified file and folder structure of its own store (not organize) ebooks and people who are used to using the traditional file and folder system for organizing have trouble accepting calibre's way of doing it. I personally like to have as much "metadata" in my file names as possible should I ever decide to abandon calibre for another program. Since computer storage space is so cheap nowdays, an easy solution is to keep both your original, klunky, kludgy file/folder system and calibre's own file/folder system and simply ignore calibre's. Worldwalker, one of the power users here, suggests treating calibre's folder system as a black box and never touch it, look at it, or even think about it.

You can get more detailed information about this in the calibre forum.

I understand how Calibre works. I use it for all my ebooks and love it. My issues were 1) that trying to organize the PDFs myself is not working well for me so I was happy to turn it over to a more efficient system but 2) I worried because Calibre is so slow, and because I don't plan to use any of the conversion or other features on these so I was afraid it would be overkill.

I'm kind of at a crossroads in regards to this as well, ficbot.
Right now I'm leaning towards using Stanza for PDFs, and iBooks for ePubs. Which means Calibre has both PDFs and ePubs in its library, iBooks has the ePubs duplicated in its iTunes Media Library, and Stanza relying on Calibre's library to store the on-computer PDF library.

I don't notice too much of a slowdown with Calibre-but I don't have anywhere near your database...I'm completely re-doing my Calibre library, and probably will end up with 65-70 ePubs and 10-15 PDFs.

The other option is to have a third, program neutral file library stored somewhere else, with the different formats saved out. I've just been so used to using Calibre's one library (shared on Dropbox with 2 computers), that having iBooks/iTunes as another library has made things a bit odd.

I'm curious as to how other people are storing/cataloging their eBook collections outside their devices. In some ways, pure Kindle/Nook users have it simple-let Amazon and B&N deal with it .

Since I got the iPad, I have been reading more PDF-type stuff. I was keeping it separate in its own little PDF folder because I was worried large files would gum up Calibre, which has never been very speedy on my machine and is already pushing 900 entries just of novels and proper books. But it is getting out of hand, I am finding it hard to locate things swiftly and identify what is on the iPad and what is not. I have too many sub-folders. It is getting unwieldy.

I don't want to convert these files or use Calibre features like that. I just want to have them all in one central place where I can search, sort and load onto iBooks. Most of them are magazine scans, and a few textbook-type stuff. Some of them are short (specific magazine articles I have scanned) and some are full-length books.

If Calibre is not the solution, is there something else? Or should I just put them into Calibre with the rest of my ebook stuff?

Calibre doesn't care how big the file is—it's just a filename, metadata and a location to it. It won't gum up the works any more than a 5k text document would.

I have 10,000+ books in my library. I use Calibre to keep some sort of overview, and use its Save to Disk feature to build and populate the folder structure I want on my reader.
The latest version of Calibre still needs several minutes to start with a large library like this, and I find that Save to Disk is very slow (although part of the problem is my rather old computer). For the rest I have no performance problem. Searching and filtering is very fast.